Faecal phageome of healthy individuals: presence of antibiotic resistance genes and variations caused by ciprofloxacin treatment

Fernández‐Orth, Dietmar; Miró, Elisenda; Brown-Jaque, Maryury; Rodríguez-Rubio, Lorena; Espinal, Paula; Rodríguez-Navarro, Judith; González-López, Juan José; Muniesa, Maite; Navarro, Ferrán

doi:10.1093/jac/dky540

Cited by 28 publications

(32 citation statements)

References 66 publications

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“…This procedure, together with the limited number of phages in some of the samples, meant that sufficient DNA concentration and purity for the metagenomic analysis was only obtained in five pools of samples. Nevertheless, the viromes analyzed showed a far greater abundance of phages infecting a wider range of bacterial genera than in our previous study 18 . Phage identification was based on Kraken results, which in turn were based on database sequences.…”

Section: Discussioncontrasting

confidence: 68%

“…In contrast, serum samples were more concentrated and easier to handle than blood, and phage prevalence detected in sera was markedly higher. The Siphoviridae morphological type was the most common group, as previously reported 15,18,27 . Siphoviridae detection could have been underestimated in a percentage of samples showing icosahedral phage capsids compatible with Siphoviridae morphology but without a tail, which prevented their correct classification 18,[28][29][30] .…”

Section: Discussionsupporting

confidence: 63%

“…In contrast, a more detailed picture of the diversity of phages in the samples was provided by the virome analysis. The multi-step phage DNA purification protocol was previously validated to guarantee that only DNA within viral capsids was evaluated 18 . This procedure, together with the limited number of phages in some of the samples, meant that sufficient DNA concentration and purity for the metagenomic analysis was only obtained in five pools of samples.…”

Section: Discussionmentioning

confidence: 99%

“…Four pools of urine samples and one pool of ascitic fluid (AF) samples allowed the recovery of viral DNA in sufficient quantity and purity to generate the libraries. Before the capsids were broken, the samples were tested for 16S rRNA genes, and negative results confirmed the absence of non-packaged DNA and the effectiveness of the protocol 18 . Analysis of the virome showed a great number of unclassified sequences, that was greater in the AF and in two urine pool samples (Table 2), but the abundance of unclassified sequences did not correlate with the number of phages detected.…”

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confidence: 99%

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Unravelling the consequences of the bacteriophages in human samples

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Fernández‐Orth

Brown-Jaque

et al. 2020

Sci Rep

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Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. to unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. in addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. this method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs. Bacteriophages (phages), viruses that infect bacteria 1 , are probably the most abundant entities in the world 2. The abundance of phages in the human body is beginning to be envisaged as having a critical influence on human health. The ability of phage communities to modify and regulate bacterial communities 3,4 suggests that phages are to some extent responsible for the homeostasis of the microbiota 5,6. Phages can contribute to bacterial genomic plasticity by horizontal gene transfer (transduction) 7,8 , which may benefit the metabolism 9 or affect the virulence of the bacterial host 10,11. Some phages produce transducing particles consisting of phage capsids that carry only bacterial DNA 12,13 , these transducing particles or elements similar to gene transfer agents (GTAs) 14 are thought to be mechanisms used by bacterial cells to spread their own genomic content 12. The existence of phages in human biomes presupposes their presence in human samples and their contamination of laboratory cultures initiated from these samples 15. This interference can be envisaged at two levels: 1) phages may propagate in enriched liquid culture media (used to enhance analytical sensitivity and selectively propagate the pathogen) by infecting bacteria (the pathogen targeted for isolation) and causing their lysis during the process; and 2) phages can transport bacterial DNA, including virulence genes such as toxins 16 , antibiotic resistance genes (ARG) 11,17,18 or bacterial 16S rRNA genes 18. If any of these genes are targeted by molecular methods, positive results can be a confounding factor in the interpretation of results 19. The confirmation of phage interference in microbiological diagnosis, as envisaged in prev...

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Section: Discussioncontrasting

confidence: 68%

Section: Discussionsupporting

confidence: 63%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Unravelling the consequences of the bacteriophages in human samples

Blanco-Picazo

Fernández‐Orth

Brown-Jaque

et al. 2020

Sci Rep

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“…Transduction is common in WWTPs as a result of high bacterial and viral density, and it is estimated that each hour thousands of transductions occur in these environments (Rizzo et al, 2013;Lood et al, 2017). Therefore, in certain environments, it is possible that viruses may be associated with ARG transfer (Fernández-Orth et al, 2019). In addition, recent work has suggested phageinducible chromosomal islands are widespread amongst bacteria, facilitating transduction of ARGs and virulence factors (Chen et al, 2015;Novick and Ram, 2016;Martínez-Rubio et al, 2017;Fillol-Salom et al, 2018).…”

Section: Associations Between Args Viruses and Bacteriamentioning

confidence: 99%